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Human sorting nexin 7, phox homology (PX) domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OCS PDB ENTRY 1OCS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277 2M AmmoniumSulfate, 0.1M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.77 55.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.3 α = 90 b = 57.3 β = 90 c = 97.1 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm Multilayer mirror 2009-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.03790 MAX II I911-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.7 30 99.6 0.087 0.143 13.1 3.5 39129 39129
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.8 99.7 0.561 0.636 2.8 3.4 6200
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1OCS 1.7 28.65 37168 37168 1957 100 0.1663 0.16638 0.16464 0.1726 0.19963 0.2054 RANDOM 12.07
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.29 0.14 0.29 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.105 r_dihedral_angle_4_deg 15.211 r_dihedral_angle_3_deg 11.504 r_dihedral_angle_1_deg 5.393 r_scangle_it 4.558 r_scbond_it 2.745 r_mcangle_it 1.823 r_angle_refined_deg 1.497 r_mcbond_it 1.002 r_angle_other_deg 0.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.105 r_dihedral_angle_4_deg 15.211 r_dihedral_angle_3_deg 11.504 r_dihedral_angle_1_deg 5.393 r_scangle_it 4.558 r_scbond_it 2.745 r_mcangle_it 1.823 r_angle_refined_deg 1.497 r_mcbond_it 1.002 r_angle_other_deg 0.832 r_mcbond_other 0.249 r_chiral_restr 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2078 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 67
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling